On 7/11/06, [EMAIL PROTECTED]
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From: "Berk Hess" <[EMAIL PROTECTED]>
Subject: Re: [gmx-users] Energy profile with umbrella sampling
>From: "pim lists" < [EMAIL PROTECTED]>
>>We are using umbrella sampling to observe a hydrogen transfer. And would
>>like to analyze our results by graphing the energy against the reaction
>>coordinates, in order to see the energy profile for the transition state.
>>Does the force constant from the umbrella sampling affect the output of
>>g_energy? Are there any special steps that should be taken in order to do
>>this?
>>
>>Thank you for your time and assistance
>>
>>Robert Fiske
>>
>
>According to src/mdlib/pull.c the umbrella forces*displacement are added to
>the virial. Therefore I'd say you see back effects in the virial/pressure
>output of g_energy.
>The umbrella potential energy is apparently not written away anywhere,
>you'll have to recalculate it from the displacement-from-the-mean written
>in
>your pull.pdo output file, and add that energy yourself to the total
>energy.
Indeed it does not seem to be added to the total energy,
this should be stated in the manual.
But anyhow, in most cases you do not want this contribution to the energy,
as you would like to have the energy of the original system.
The only thing that you need to correct for is that the sampling
is biased by the umbrella potential, which you can recalculate from
the displacement and the force constant.
Berk.
Sorry, I must have been sleeping! In any case, you state you want an energy profile for the transition state. Interaction energies you can get correctly from the g_energy file, but I guess you want free energies. How could you retrieve those? Boltzmann inversion of the distance distribution of your coordinate + the correction of the umbrella potential?
greetings, Pim
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